LI-COR ODYSSEY Series User manual

®
Operator’s Manual

CE Marking:
This product (model number 9260) is a CE-marked product. For conformity information, contact
LI-COR Support at http://www.licor.com/biotechsupport. Outside of the U.S., contact your local sales
office or distributor.
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Note on Safety
LI-COR products have been designed to be safe when operated in the manner described in this manual. The safety
of this product cannot be guaranteed if the product is used in any other way than is specified in this manual. The
Odyssey® Sa Imager is intended to be used by qualified personnel. Read this entire manual before using the
Odyssey Sa Imager.
Equipment Markings:
The product is marked with this symbol when it is necessary for you to refer to the
manual or accompanying documents in order to protect against damage to the product.
The product is marked with this symbol when a hazardous voltage may be present.
Manual Markings:
WARNING Warnings must be followed carefully to avoid bodily injury.
CAUTION Cautions must be observed to avoid damaging your equipment.
NOTE Notes contain additional information and useful tips.
IMPORTANT Information of importance to prevent procedural mistakes in the operation of the
equipment or related software. Failure to comply may result in a poor experimental
outcome but will not cause bodily injury or equipment damage.
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Notice
The information contained in this document is subject to change without notice.
LI-COR BIOSCIENCES MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL,
INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANT-ABILITY AND
FITNESS FOR A PARTICULAR PURPOSE. LI-COR Biosciences shall not be liable for errors contained herein or for
incidental or consequential damages in connection with the furnishing, performance, or use of this material.
This document contains proprietary information which is protected by copyright. All rights are reserved. No part of
this document may be photocopied, reproduced, or translated to another language without prior written consent of
LI-COR, Inc.
Printing History
Publication Number: 977-19469
Revised: April 2011
Revised: June 2011
Revised: April 2013
Revised: April 2014
Revised: December 2020
LI-COR Biosciences is an ISO 9001:2015 registered company. © 2015 LI-COR, Inc. Specifications subject to change.
LI-COR, Odyssey, Image Studio, and IRDye are registered trademarks of LI-COR, Inc. in the United States and other
countries. All other trademarks belong to their respective owners. The Odyssey Infrared Imaging Systems and IRDye
reagents are covered by U.S. patents, foreign equivalents, and patents pending.
Federal Communications Commission Radio Frequency Interference Statement
WARNING: This equipment generates, uses, and can radiate radio frequency energy and if not installed in
accordance with the instruction manual, may cause interference to radio communications. It has been tested and
found to comply with the limits for a Class A computing device pursuant to Subpart J of Part 15 of FCC rules,
which are designed to provide a reasonable protection against such interference when operated in a commercial
environment. Operation of this equipment in a residential area is likely to cause interference in which case the
user, at his own expense, will be required to take whatever measures may be required to correct the interference.
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Global Headquarters
4647 Superior Street • Lincoln, NE 68504
Toll free: 800-645-4267 • Fax: [phone] • [e-mail] •licor.com/bio
Regional Offices
LI-COR Biosciences GmbH
Siemensstraße 25A • 61352 Bad Homburg • Germany
Phone: [phone] • Fax: [phone] • [e-mail]
LI-COR Biosciences UK Ltd.
St. John’s Innovation Centre • Cowley Road
Cambridge • CB4 0WS
United Kingdom • Phone: [phone] • Fax: [phone] • [e-mail]
LI-COR Biotechnology Distributor Network: www.licor.com/bio/distributors
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Chapter 1: Safety and Operational Information
In This Manual... 9
Safety Considerations 9
Laser Safety 9
Safety Interlocks 10
Placement in the Laboratory 11
Ambient Laboratory Conditions 11
Ventilation 11
Space Requirements 11
Removing the Laser/Microscope Assembly Shipping Lock 11
Moving the Imager 11
Level the Imager 11
Electrical Considerations 12
Power Cords 12
Fuse Replacement 12
Routine Maintenance 12
Chapter 2: Overview and General Description
Buttons and Indicator Lights 15
Power Button 15
Using the Power Button to Reset the Odyssey Sa Imager 15
Eject Button 15
Using the Eject Button to Reset Network Parameters 16
Indicator Lights 16
Back Panel Connectors 16
Hardware Description 16
Scanning and Detection Hardware 16
Odyssey Sa Server and Server Software 17
Chapter 3: Operation
Selecting Microplates 19
Microplate Compatibility 19
Determining Focus Offset 20
Scanning Microplates 20
Odyssey® Sa
Imager
Table of Contents
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Loading Microplates for Standard Scans 20
Starting Microplate Scans 21
Scanning Membranes in the Membrane Carrier 21
Loading a Membrane 21
Scanning Membranes 22
Scanning Gels in the Membrane Carrier 23
Using the Bar Code Reader (Optional Accessory) 23
Chapter 4: Assembling the Odyssey Sa System
Introduction 25
Import the Odyssey Sa Express Software Key 25
Assembling the Odyssey Sa System 25
Adding Users 27
Configuring Automatic IP Addressing 27
Reset to Automatic IP Addressing 28
Chapter 5: Installing a BioTek® BioStack™ Plate
Stacker
Introduction 31
Installation Summary 31
Initial Odyssey Sa Setup 32
Initial BioStack Setup 32
Connecting Power and Communication Cables 34
Leveling the Odyssey Sa Imager 35
Installing the Locator Clamp 36
Leveling the BioStack™ Plate Stacker 37
Connecting the BioStack Plate Stacker to the Locator 39
BioStack X-Y Alignment 41
BioStack Z-Axis Training 43
Express Run Errors Related to the BioStack Plate Stacker 46
Chapter 6: Appendix
Specifications 49
Laser/Microscope 49
Operating Specifications 49
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Chapter 1: Safety and Operational Information
In This Manual...
The following topics are discussed in this manual:
lSafety considerations.
lInstrument placement and power considerations.
lDescription of detection optics and signal processing.
lOperation of the Odyssey® Sa Imager.
Safety Considerations
Laser Safety
The Center for Devices and Radiological Health (CDRH) was established in October, 1982, by the
U.S. Food and Drug Administration (FDA) to protect the public health in the fields of medical
devices and radiological health.
Manufacturers of products subject to performance standards under the Radiation Control for Health
and Safety Act of 1968 are required to furnish various reports to the CDRH.
The Odyssey Sa Infrared Imaging System is certified as a Class I laser product, containing a Class
IIIb laser. This means that hazardous laser radiation is not emitted outside the instrument.
Radiation emitted inside the instrument is confined within protective housings and external covers.
The laser beam cannot escape during any phase of user operation.
The CDRH implemented regulations for laser products on August 1, 1976 (CDRH radiation
performance standard 21, Code of Federal Regulations Chapter 1, Subchapter J). Compliance for
products marketed in the United States is mandatory. The label that must be attached to laser
products marketed in the United States is Figure 1-1 and is located on the rear panel of the
Odyssey® Sa Imager, indicating compliance with CDRH regulations.
CAUTION: Use of controls or adjustments or performance of procedures other than those specified
herein may result in hazardous radiation exposure.
The Odyssey Sa Infrared Imaging System contains two lasers: one emitting at 785 nm and one at
685 nm. The 685 nm laser emits visible laser radiation – direct exposure to either beam may cause
eye damage. Laser radiation is emitted through apertures at the top of the microscope assembly,
inside the instrument enclosure.
Odyssey® Sa
Imager
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Chapter 1: Safety and Operational Information
Safety Interlocks
There are no user serviceable parts inside the Odyssey®Sa Imager and it is not recommended that
users open the instrument enclosure.
When the top panel of the instrument is opened, safety interlocks immediately turn off the lasers.
Audible tones also sound when the top panel of the enclosure is opened and closed.
Figure 4-1. Back panel label of the Odyssey Sa Imager showing the following: 1) Power requirements, 2) FCC and
CDRH compliance notices, 3) Laser radiation exposure warning, and 4) Class 1 Laser Product classification.
Chemical Safety
LI-COR Biosciences recommends that all biochemicals be handled carefully, and that safe laboratory
procedures be followed at all times. Be aware of the hazards associated with any chemical before you
begin work.
The Odyssey Sa Imager should not be used with any radioactive materials.
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Odyssey® Sa Imager
Placement in the Laboratory
The Odyssey Sa Imager weighs approximately 24 kg (53 lb). When combined with the BioTek®
BioStack™ Automated Microplate Stacking System, the combined weight is about 32 kg (72 lb).
The system should be placed on a level laboratory bench that is sufficiently sturdy to bear its weight.
Ambient Laboratory Conditions
Place the Odyssey Sa Imager away from external heat sources (furnaces, windows, etc.). Additional
heating can cause high temperatures within the enclosure, resulting in instrument shut down.
Place the instrument away from sinks or other sources of water that pose a shock hazard.
Recommended operating conditions are 15-35°C and a dew point not greater than 19°C. Extended
operation outside these conditions will cause damage to the instrument.
Ventilation
The instrument enclosure and circuit boards are cooled with two internal fans. There are no
restrictions regarding placement of the instrument with respect to the fan cover; the fan shrouds are
not filtered (requires no service), and the cover serves only as an exhaust outlet.
Space Requirements
The Odyssey Sa Imager requires an area approximately 36 cm H x 45 cm W x 55 cm D (14 inches x
18 inches x 22 inches), and a vertical clearance of at least 37 cm (14"). When used with the
BioTek® BioStack™ microplate stacking system, the area required is approximately 61 x 122 cm (24
x 48").
Removing the Laser/Microscope Assembly Shipping Lock
The laser/microscope assembly moves beneath the microplate when the Odyssey Sa Imager is
scanning. It is important to lock this assembly in place during shipment to prevent any damage that
may be caused if it should bump into other hardware inside the imager. Two screws make up the
shipping lock that holds the laser/microsope assembly in place. These screws must be removed
before operating the Odyssey Sa Imager or the instrument status light will illuminate red, indicating
a malfunction. Please contact LI-COR Technical Support for help in removing these screws.
Moving the Imager
LI-COR recommends that you do not move your imager. Instead, please contact LI-COR Technical
Support for options.
LI-COR cannot be held responsible for any damage incurred while moving, transporting, or
shipping the Odyssey Sa Imager, even if an existing warranty and/or service contract applies.
LI-COR cannot be held responsible for any injury incurred while moving, transporting, or
shipping the Odyssey Sa Imager.
Level the Imager
Level the instrument to prevent the imaging drawer from scraping the lab bench or table in front of
the instrument and to keep the instrument from tilting.
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Chapter 1: Safety and Operational Information
The instrument can be leveled by turning the threaded metal inserts located in each of the 4 plastic
feet (Figure 4-2).
Instrument base
Metal insert
Plastic foot
Figure 4-2. Turn the metal inserts on the feet to adjust the height.
Electrical Considerations
Power Cords
The Odyssey® Sa Imager is equipped with a 3-wire grounding-type plug. This plug will only fit into
a grounding-type outlet. This is a necessary safety feature. If you are unable to insert the plug into
the outlet, you will need to replace the outlet. Do not defeat the purpose of the grounding-type plug.
Do not locate the Odyssey Sa Imager where the power cord will be walked on or exposed to water or
chemical spills.
The Odyssey Sa Imager draws a maximum of 2.25 amperes at 120V. If an extension cord is used,
make sure the total of the ampere ratings on the instruments plugged into the extension cord does
not exceed the extension cord ampere rating. Also make sure the total amperage of instruments
plugged into the wall outlet does not exceed the amperage capacity for the outlet. In the U.S., this is
usually 15 or 20 amperes.
Fuse Replacement
There are no user serviceable fuses inside the Odyssey Sa Imager. If the instrument fails to power
up, and you suspect that a fuse has blown, contact LI-COR Technical Support.
Routine Maintenance
The Odyssey Sa Imager requires only minimal maintenance. However, as with any equipment
utilizing electrical voltages, there is a danger of fire or electrical shock if the equipment is not
properly maintained.
LI-COR Biosciences recommends that you routinely inspect the system and follow these general
maintenance guidelines:
lWipe all chemical spills from the exterior of the case.
lClean the exterior case parts with warm water and a damp cloth. The exterior case parts are res-
istant to chemical spills, but do not use scouring compounds, solvents such as acetone, benzene,
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Odyssey® Sa Imager
carbon tetrachlorides, lacquer thinner, or alcohol to clean the case.
lInspect all cables and power cords for evidence of fraying, exposed wire, or loose connections.
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Chapter 2: Overview and General Description
Buttons and Indicator Lights
Power Button
Briefly press the power button on the front panel to start up or shut down the Odyssey® Sa
instrument. An indicator light in the power button blinks during the start-up or shut-down
procedure and is continuously on when the instrument is ready to operate.
Using the Power Button to Reset the Odyssey Sa Imager
The power button has another function beyond turning the instrument on or off. In the event that
the instrument becomes unresponsive, the instrument can be reset by pressing and holding in the
power button for five seconds. This procedure cuts power to the instrument and internal computer,
so it should only be used when communication cannot be established by any other means. Normal
operation should resume after the power button is pressed again to turn the instrument back on,
though start up may take several minutes.
Eject Button
Pressing the eject button extends or retracts the Odyssey Sa plate carrier. A protective door
automatically opens and closes as the plate carrier extends or retracts. This door protects the user
from exposure to laser radiation. Do not defeat the operation of this door.
Odyssey® Sa
Imager
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Chapter 2: Overview and General Description
Using the Eject Button to Reset Network Parameters
The eject button also has an alternate use. After pressing the power button, there is a brief period
during the startup procedure when the green scanning status light blinks. While the scanning
status light below the eject button is blinking, the network parameters can be reset to automatic IP
addressing by pressing the eject button and holding it down. Make sure the eject button is depressed
at the end of the four times that the scanning status light blinks.
Indicator Lights
Scanning Status: During normal operation, the scanning status light illuminates green when there
is a scan in progress and is off at all other times.
Instrument Status: The instrument status light is normally off, but illuminates red when there is a
malfunction in the instrument.
Contact LI-COR Technical Support if the instrument status light turns on.
Back Panel Connectors
Below the fan on the Odyssey®Sa Imager back panel are a variety of connectors for the server
hardware inside the instrument. None of these connectors should be used except the network port. The
network port is used to connect the Odyssey Sa instrument to the computer via a Cat. 5 RJ45
crossover cable (Assembling the Odyssey Sa System on page25).
The receptacle for the power cable is also located on the back panel.
Note: The power switch for the power supply on the back panel should always be in the ON
position. For normal operation, the instrument should always be powered on and off from the
power switch on the instrument front panel.
Hardware Description
Scanning and Detection Hardware
The Odyssey Sa Imager uses two solid-state diode lasers to simultaneously provide light excitation at
685 and 785 nm. Collimating lenses,optical bandpass filters, and a focusing lens focus and tune
the laser beams to produce an excitation spot on the target detection area of the microplate. The
microscope electronics modulate the laser beams to discriminate the infrared (IR) dye signal
fluorescence from background fluorescence. The scanner detection optics focus on the excitation
spot and collect light from the fluorescing IR dyes.
After collection by the microscope objective, the light is passed to a dichroic mirror. The mirror
splits the light and essentially sorts the fluorescent signals by transmitting the light from one IR dye
and reflecting light from the other IR dye. The transmitted and reflected lights travel two
independent paths through optics designed to remove scattered and stray light. The light is
ultimately focused onto one of two avalanche photodiodes that converts the light to an electrical
signal for processing by the microscope detection electronics.
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Odyssey® Sa Imager
In the microscope electronics, the signal is amplified, filtered, and finally converted to a digital value
by an analog-to-digital converter. The digital signal is demodulated, filtered again, and coordinated
with the microscope position by a Digital Signal Processor (DSP) to produce the image file.
The entire compact laser/microscope assembly travels on a platform that moves beneath the
microplate along both the X- and Y-axis. The microscope can also be adjusted along the Z-axis to
change the height of the microscope’s focal point. Changing the focus height
makes it possible for the instrument to accommodate variations in the height of the target detection
area for different brands of microplates. The focus height can be varied from 1.71 to 3.95 mm.
Odyssey Sa Server and Server Software
The Odyssey Sa Imager contains a server that controls scanning, data storage, and communication
with Image Studio™Software. The Odyssey Sa server has a pre-installed copy of Odyssey Sa Server
software. This software is periodically updated with new releases that are posted on LI-COR
Biosciences’ web site. Users will be contacted with download instructions when new releases are
available.
The Odyssey Sa server communicates with the computer via TCP/IP in a stand-alone configuration.
When a scan is started from the Image Studio software, scan parameters are sent to the Odyssey Sa
server, which starts the scan, collects the data, stores the data in its internal hard disk, and sends a
copy of the scanned images to Image Studio software for analysis and storage on a hard disk in the
computer.
Note: The Odyssey Sa Imager should be used for temporary storage only; when the hard disk is full, the
oldest files are overwritten to make space.
Files on the internal hard disk are stored in scan groups. Scan groups are like folders, but access is
restricted to users that have been given permission to use the scan group. The Odyssey Sa Imager
uses password protected user accounts to establish the access rights for each user.
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Chapter 3: Operation
Selecting Microplates
Microplates must meet certain physical characteristics to be scanned by the Odyssey Sa Imager.
Proper selection of microplates significantly affects the results of your analysis as each plate has its
own characteristics including well depth, plate autofluorescence, and well-to-well signal crossover.
Some general considerations for microplate selection are provided below and some of the Odyssey
Sa application protocols give more specific microplate recommendations.
Microplate Compatibility
The In-Cell Western™ Assay uses detection at the well surface with no liquid present. This results
in minimal well-to-well signal spread, allowing the use of both clear as well as black-sided plates
with optically clear bottoms. For assays that involve imaging of a liquid, plates that have black walls
and clear bottoms should be used to avoid well-to-well signal spread. Do not use plates with white
walls since the autofluorescence from the white surface will create significant noise.
The Odyssey Sa microplate carrier supports both normal height and deep-well microplates
conforming to the following standards:
ANSI/SBS 1-2004 Microplates - Footprint Dimensions
ANSI/SBS 2-2004 Microplates - Height Dimensions
ANSI/SBS 3-2004 Microplates - Bottom Outside Flange Dimensions
ANSI/SBS 4-2004 Microplates - Well Positions
Note: The ANSI/SBS standards can be found on the Internet at http://www.sbsonline.org.
The ANSI/SBS standards specify standard dimensions for plates, but some plates conforming to
these dimensions may still not be compatible. Plates vary in the location and thickness of the well
bottoms, which can result in the Odyssey Sa Imager not being able to focus in the correct position.
Some plate materials are also not sufficiently transparent or may produce high background
fluorescence. When choosing a brand of plate, test it to make sure you have sufficient fluorescent
intensity from the samples and that the background fluorescence from the plate is low.
The following plates are recommended by LI-COR Biosciences:
96-well format Nunc® (P/N 161093 or165305)
96-well format Falcon™ (P/N 353075 or 353948)
384-well format Nunc (P/N 164688 or 164730)
384-well format Falcon (P/N 353961 or 353962)
To be compatible with the Bio-Tek® Bio-Stack™ Microplate Stacking System, microplates should
have standard dimensions:
Odyssey® Sa
Imager
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Chapter 3: Operation
Width: 3.365" (85.47 mm) +/0.015" (0.38 mm) at the corners
Length: 5.030" (127.76 mm) +/- 0.015" (0.38mm) at the corners
Height: 0.565" (14.35 mm) +/- 0.010" (0.254 mm)
Note: The Odyssey®Sa Imager does support deep-well microplates, but the Bio-Stack does not.
Determining Focus Offset
The Odyssey Sa Imager requires that microplates have a maximum of 4.0 mm distance from the
base of the microplate to the target detection area of the plate. When using the plates specified
above, the recommended starting point for the focus offset is 3.0 mm.
The optimal focus offset for these plates or other plates can be determined by scanning a plate
containing experimental and control samples at 1.7, 2.0, 3.0, and 4.0 mm focus offsets. Use the same
intensity settings for each scan. After reviewing the collected scans, use the focus offset with the
highest signal-to-noise for experiments.
Scanning Microplates
Loading Microplates for Standard Scans
Before scanning, clean the bottom plate surface with a moist, lint- free paper to remove any
obstructions during scanning.
Protect plates from light before scanning to ensure highest sensitivity. When storing plates after
scanning, the plates should remain protected from light at room temperature.
1) Press the eject button on the Odyssey Sa Imager front panel to open the microplate carrier.
2) Orient the microplate with well A1 aligned with the A1 marker on the microplate carrier.
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